Are microbial communities indicators of soil health in a dryland wheat cropping system?

Authors: Schlatter, Daniel; Hansen, Jeremy; Carlson, Bryan; Leslie, Ian; Huggins, David; Paulitz, Timothy

Submitted to: Applied Soil Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/29/2021
Publication Date: 2/1/2022
Citation: Schlatter, D.C., Hansen, J.C., Carlson, B.R., Leslie, I.N., Huggins, D.R., Paulitz, T.C. 2022. Are microbial communities indicators of soil health in a dryland wheat cropping system? Applied Soil Ecology. 170. Article 104302. https://doi.org/10.1016/j.apsoil.2021.104302.
DOI: https://doi.org/10.1016/j.apsoil.2021.104302

Interpretive Summary: Although soil health measurements are increasingly recognized as an important tool for evaluating the impacts of agricultural practices, the biotic components of soil health are poorly understood. Microbial communities are crucial drivers of soil health, but are often considered a ‘black box’ due to their immense diversity. We used high-throughput DNA sequencing to characterize the composition and diversity of soil microbial communities and correlated microbial populations with soil chemical variables, soil health measures, and crop yields at two soil depths in fields managed with aspirational (no-till) or business-as-usual (conventional) practices. We found that although soil health measures did not differ between fields, microbial communities were distinct between fields and soil depths. Further, we identified specific microbial groups that were associated with soil health measurements and crop yields. This work suggests that microbial communities are sensitive indicators of agricultural management and that specific microbial groups may be useful indicators of soil health.

Technical Abstract: Soil health is an increasingly important concept that provides aspirational targets for agricultural management. Due in part to the incredible diversity of soil microbial communities, however, the biological components of soil health remain poorly understood. In the last decade the refinement of high-throughput DNA sequencing approaches for examining soil microbial communities has led to sequence-variant resolution insights into their diversity. In this work we employ high-throughput sequencing of bacterial (16S rRNA genes) and fungal (internal transcribed spacer [ITS]) regions to evaluate soil microbial communities in soil in relation to other soil chemical parameters, biological soil health tests, and crop yields in fields under long-term reduced tillage (business-as-usual) and no tillage (aspirational) management at two soil depths. We found that tillage systems and soil depth were crucial determinants of microbial community composition and diversity in conjunction with soil chemical measures. Moreover, although some measures of biological soil health (CO2-burst, Haney Soil Health Score) did not differentiate fields under reduced tillage and no-till systems, amplicon sequencing revealed clear differences in microbial communities between management regimes. The relative abundances of many microbial taxa were significantly related to soil chemical variables and crop yields. Fungal communities showed stronger correlations with yield than bacterial communities. Fungi from the families Sordariaceae, Hydnodontaceae, Hypocreaceae, and Clavicipitaceae were positively correlated with yield, especially in the upper soil depth, while Glomeraceae and Phaeosphaeriaceae were negatively correlated. Many of these correlations were also seen in the subsequent winter wheat and chickpea crops, and some correlations could be detected in the 20-year previous yield history of the no-tillage farm. Among the bacteria, only Microbaceriaceae and Xanthomonadaceae were positively correlated, but Caulobacteriaceae, Flavobacteriaceae, Sphingobacteriaceae, Chitinophagaceae were more abundant in lower yielding locations. This may reflect the strong plant selection in the rhizosphere for these bacterial groups in stressed plants. There were no significant differences, however, between microbial diversity and management practices or significant correlations with crop yields. These results suggest that some specific groups of microbial taxa are responsive to tillage systems, exhibit positive relationships with grain yields, and may be useful indicators of soil health.